Aerobic Methanotrophy and Nitrification: Processes and Connections


Ammonia and methane are structurally similar molecules. Not surprisingly therefore, microorganisms that use methane as a sole energy source (methanotrophs) and microorganisms that use ammonia as a sole energy source (ammonia oxidisers or nitrifiers) share many similarities. They have several key enzymes in common, most especially the ammonia monooxygenase/particulate methane monooxygenase enzyme family. The two groups are proposed to have a common evolutionary history. They occupy similar ecological niches, and compete for nitrogen. Enzymatically, nitrifiers are capable of methane oxidation, and methanotrophs are capable of nitrification. Microbial ecologists have attempted to find specific inhibitors for either group in order to study their respective roles in the environment. The contribution of ammonia oxidisers to methanotrophy in natural systems appears to be very minor, however methanotrophs may sometimes have important roles in the nitrogen cycle.

Key Concepts:

  • Some bacteria and archaea are capable of using methane or ammonia as energy sources.

  • Methanotrophs and ammonia oxidisers are each highly specialised to living on their particular substrate.

  • Methanotrophs and ammonia oxidisers have several key enzymes in common, and may share a common evolutionary history.

  • Both groups must cope with toxic by‐products of ammonia oxidation.

  • Methanotrophs may be important in the environmental nitrogen cycle, but ammonia oxidisers do not affect the methane cycle.

  • Ammonia oxidising archaea appear to outcompete ammonia oxidising bacteria under ammonia‐limiting and acidic conditions.

Keywords: methane; ammonia; nitrification; methanotrophy; ammonia oxidation; nitrous oxide; denitrification; chemolithotrophy; biogeochemistry

Figure 1.

Overlapping pathways for ammonia and methane oxidation. Black lines denote bacterial pathways; grey lines denote putative pathways for ammonia‐oxidising thaumarchaea. Enzymes catalysing each process are: a, ammonia/methane monooxygenase; b, hydroxylamine oxidoreductase; c, nitrite reductase; d, nitric oxide reductase; e, methanol dehydrogenase; f, formaldehyde dehydrogenase; g, formate dehydrogenase; h, enzymes of the serine or ribulose monophosphate pathway and i, enzymes of the Calvin–Benson–Bassham cycle. The question marks in the thaumarchaeal pathway denote uncertainty regarding the intermediate produced by ammonia monooxygenase, the enzyme that oxidises this intermediate to nitrite, and enzymes that form NO/N2O from the intermediate of ammonia oxidation or from reduction of nitrite as measured by Santoro et al. . The dashed line denotes a possible role of NO in ammonia‐oxidation (Schleper and Nicol, ).

Figure 2.

Phylogenetic tree of partial (495 nucleotides) pmoA/amoA gene sequences of major groups of ammonia oxidisers and methanotrophs. The accession numbers of the sequences used to create the tree are shown. The tree was constructed with TREE_PUZZLE, a quartet maximum‐likelihood method, using a Schoeniger–von Hasseler distance calculation (Schmidt et al., ). Support values for major nodes are given, and multifurcations are drawn when the support for a bifurcation is <50%. The bar represents 0.2 changes per nucleotoide position.



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Ward BB, Arp DJ and Klotz MG (eds) (2011) Nitrification. Washington, DC: ASM Press.

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Stein, Lisa Y, Roy, Réal, and Dunfield, Peter F(Apr 2012) Aerobic Methanotrophy and Nitrification: Processes and Connections. In: eLS. John Wiley & Sons Ltd, Chichester. [doi: 10.1002/9780470015902.a0022213]